Domestication drive the changes of immune and digestive system of Eurasian perch (<i>Perca fluviatilis</i>)

<div><p>Domestication has altered a variety of traits within the Eurasian perch (<i>Perca fluviatilis</i>), including phenotypic, physiological and behavioral traits of Eurasian perch (<i>Perca fluviatilis</i>). Little is known, however, about the genetic changes between domesticated and wild Eurasian perch. In this study, we assembled a high-quality <i>de novo</i> reference transcriptome and identified differentially expressed genes between wild and domesticated Eurasian perch. A total of 113,709 transcripts were assembled, and 58,380 transcripts were annotated. Transcriptomic comparison revealed 630 differentially expressed genes between domesticated and wild Eurasian perch. Within domesticated Eurasian perch there were 412 genes that were up-regulated including <i>MHCI</i>, <i>MHCII</i>, <i>chia</i>, <i>ighm</i> within immune system development. There were 218 genes including <i>try1</i>, <i>ctrl</i>, <i>ctrb</i>, <i>cela3b</i>, <i>cpa1</i> and <i>cpb1</i>, which were down-regulated that were associated with digestive processes. Our results indicated domestication drives the changes of immune and digestive system of Eurasian perch. Our study not only provide valuable genetic resources for further studies in Eurasian perch, but also provide novel insights into the genetic basis of physiological changes in Eurasian perch during domestication process.</p></div

Summary statistics of Eurasian perch transcriptome.

<p>Summary statistics of Eurasian perch transcriptome.</p

Expression profiles of 16 differentially expressed genes from RNA-Seq (red) and qRT-PCR (blue) between domesticated and wild perch.

<p>“D” indicates domesticated perch and “W” indicates wild perch.</p

Protein digestion and absorption pathway of Eurasian perch transcriptome.

<p>Genes in blue boxes indicated these genes were identified and annotated in Eurasian perch transcriptome. Genes in green boxes indicated down-regulated genes in domesticated perch.</p

Antigen processing and presentation pathway of Eurasian perch transcriptome.

<p>Genes in blue boxes indicated these genes were identified and annotated in Eurasian perch transcriptome. Genes in red boxes indicated up-regulated genes in domesticated perch.</p

Putative SNP markers differentiating domesticated and wild perch with the associated GO process.

<p>The appropriate GO process is distinguished as follows: growth (GO:0040007), immune system process (GO:0002376), and response to stimulus (GO:0050896) from the reference transcriptome^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0172903#t002fn001" target="_blank">*</a>}.</p